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- PDB-7ahu: Anti-FX Fab of mim8 in complex with human FXa -

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Basic information

Entry
Database: PDB / ID: 7ahu
TitleAnti-FX Fab of mim8 in complex with human FXa
Components
  • (Anti-FX Fab of mim8 ...) x 2
  • (Coagulation factor ...Coagulation) x 2
KeywordsBLOOD CLOTTING / Fab / anti-FX / HYDROLASE / mim8
Function / homology
Function and homology information


coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of leukocyte chemotaxis / positive regulation of TOR signaling / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation ...coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of leukocyte chemotaxis / positive regulation of TOR signaling / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / phospholipid binding / Golgi lumen / blood coagulation / positive regulation of cell migration / external side of plasma membrane / endoplasmic reticulum lumen / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain ...Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Chem-0GJ / Coagulation factor X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsJohansson, E.
CitationJournal: Blood / Year: 2021
Title: A factor VIIIa-mimetic bispecific antibody, Mim8, ameliorates bleeding upon severe vascular challenge in hemophilia A mice.
Authors: Ostergaard, H. / Lund, J. / Greisen, P.J. / Kjellev, S. / Henriksen, A. / Lorenzen, N. / Johansson, E. / Roder, G. / Rasch, M.G. / Johnsen, L.B. / Egebjerg, T. / Lund, S. / Rahbek-Nielsen, H. ...Authors: Ostergaard, H. / Lund, J. / Greisen, P.J. / Kjellev, S. / Henriksen, A. / Lorenzen, N. / Johansson, E. / Roder, G. / Rasch, M.G. / Johnsen, L.B. / Egebjerg, T. / Lund, S. / Rahbek-Nielsen, H. / Gandhi, P.S. / Lamberth, K. / Loftager, M. / Andersen, L.M. / Bonde, A.C. / Stavenuiter, F. / Madsen, D.E. / Li, X. / Holm, T.L. / Ley, C.D. / Thygesen, P. / Zhu, H. / Zhou, R. / Thorn, K. / Yang, Z. / Hermit, M.B. / Bjelke, J.R. / Hansen, B.G. / Hilden, I.
History
DepositionSep 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Anti-FX Fab of mim8 light chain
H: Anti-FX Fab of mim8 heavy chain
A: Anti-FX Fab of mim8 light chain
B: Anti-FX Fab of mim8 heavy chain
C: Coagulation factor X
D: Coagulation factor X
E: Coagulation factor X
F: Coagulation factor X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,74112
Polymers162,8698
Non-polymers8724
Water7,999444
1
L: Anti-FX Fab of mim8 light chain
H: Anti-FX Fab of mim8 heavy chain
C: Coagulation factor X
D: Coagulation factor X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8716
Polymers81,4354
Non-polymers4362
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Anti-FX Fab of mim8 light chain
B: Anti-FX Fab of mim8 heavy chain
E: Coagulation factor X
F: Coagulation factor X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8716
Polymers81,4354
Non-polymers4362
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.130, 105.250, 145.780
Angle α, β, γ (deg.)90.000, 89.995, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "L"
d_1ens_2chain "B"
d_2ens_2chain "H"
d_1ens_3chain "C"
d_2ens_3chain "E"
d_1ens_4(chain "D" and resid 254 through 304)
d_2ens_4chain "F"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLUCYSC1 - 216
d_21ens_1GLUCYSA1 - 216
d_11ens_2GLUTYRD1 - 222
d_21ens_2GLUTYRB1 - 222
d_11ens_3ILETHRE1 - 234
d_12ens_30GJ0GJF
d_21ens_3ILETHRH1 - 234
d_22ens_30GJ0GJI
d_11ens_4LEUGLUG2 - 52
d_21ens_4LEUGLUJ1 - 51

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4

NCS oper:
IDCodeMatrixVector
1given(-0.998917473666, 0.0465109137404, -0.000784670777442), (-0.0464818750342, -0.998670094738, -0.0223041962259), (-0.00182101578636, -0.0222435783771, 0.999750922541)34.0250150551, -52.4693323302, -12.3928365834
2given(-0.999958296664, 0.00870222272151, -0.00277060515977), (-0.00864767241956, -0.99977966252, -0.0191270534255), (-0.00293644257052, -0.0191022964777, 0.999813222344)32.0334160156, -53.3382833612, -12.5733012082
3given(-0.999607919346, -0.0239634152857, -0.0144831733179), (0.0248674226466, -0.997519726824, -0.0658483552419), (-0.0128692996091, -0.0661826965678, 0.997724527013)32.3268412488, -51.659215616, 12.2207805808
4given(-0.999687157666, -0.0236698793159, 0.00808230232787), (0.0229172516332, -0.99627724663, -0.0831050385012), (0.0100193001415, -0.0828938155708, 0.996508017512)31.0993053501, -50.7763299953, 11.898710593

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Components

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Coagulation factor ... , 2 types, 4 molecules CEDF

#3: Protein Coagulation factor X / Factor X / Stuart factor / Stuart-Prower factor


Mass: 27201.061 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F10 / Production host: Escherichia coli (E. coli) / References: UniProt: P00742, coagulation factor Xa
#4: Protein Coagulation factor X / Factor X / Stuart factor / Stuart-Prower factor


Mass: 6478.385 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F10 / Production host: Escherichia coli (E. coli) / References: UniProt: P00742, coagulation factor Xa

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Antibody , 2 types, 4 molecules LAHB

#1: Antibody Anti-FX Fab of mim8 light chain


Mass: 23721.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK / Production host: Homo sapiens (human)
#2: Antibody Anti-FX Fab of mim8 heavy chain


Mass: 24033.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 448 molecules

#5: Chemical ChemComp-0GJ / L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide


Type: peptide-like / Mass: 395.862 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28ClN6O5
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 444 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium acetate, 0.1 M sodium cacodylate, pH 6.5, 18 % (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→48.59 Å / Num. obs: 58767 / % possible obs: 99.9 % / Redundancy: 5.2 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1209 / Rpim(I) all: 0.05869 / Rrim(I) all: 0.1346 / Net I/σ(I): 12.31
Reflection shellResolution: 2.6→2.693 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.024 / Num. unique obs: 30703 / CC1/2: 0.523 / CC star: 0.829 / Rpim(I) all: 0.4933 / Rrim(I) all: 1.138 / % possible all: 99.97

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
PHENIX1.18_3845refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I1K,1G2L

5i1k

1g2l


Resolution: 2.6→48.59 Å / Cross valid method: FREE R-VALUE / σ(F): 1.69 / Phase error: 27.7866
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2633 3935 3.42 %
Rwork0.2027 111012 -
obs0.2139 58766 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.5 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11145 0 52 444 11641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011411443
X-RAY DIFFRACTIONf_angle_d1.880215503
X-RAY DIFFRACTIONf_chiral_restr0.09151705
X-RAY DIFFRACTIONf_plane_restr0.01181995
X-RAY DIFFRACTIONf_dihedral_angle_d13.74621577
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CX-RAY DIFFRACTIONTorsion NCS1.28498897759
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS0.891639126854
ens_3d_2EX-RAY DIFFRACTIONTorsion NCS1.07232907484
ens_4d_2FX-RAY DIFFRACTIONTorsion NCS1.26438653942
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.640.33281980.30175674X-RAY DIFFRACTION96.2
2.64-2.690.30341980.29745528X-RAY DIFFRACTION96.19
2.69-2.740.36341900.29765592X-RAY DIFFRACTION96.23
2.74-2.80.33581910.27925490X-RAY DIFFRACTION96.25
2.8-2.860.38232000.28855583X-RAY DIFFRACTION96.19
2.86-2.930.36372000.27595555X-RAY DIFFRACTION96.17
2.93-30.31311950.26585569X-RAY DIFFRACTION96.2
3-3.080.32671990.2555455X-RAY DIFFRACTION96.04
3.08-3.170.29692020.2465620X-RAY DIFFRACTION96.08
3.17-3.280.32612000.22955550X-RAY DIFFRACTION96.2
3.28-3.390.29831890.22525546X-RAY DIFFRACTION96.2
3.39-3.530.33691830.21015549X-RAY DIFFRACTION96.24
3.53-3.690.28261920.20945477X-RAY DIFFRACTION96.02
3.69-3.880.25791950.19935587X-RAY DIFFRACTION96.11
3.88-4.130.24881990.18465552X-RAY DIFFRACTION96.01
4.13-4.440.23721890.1745551X-RAY DIFFRACTION96.17
4.45-4.890.19182020.16065552X-RAY DIFFRACTION95.81
4.89-5.60.24671960.17295525X-RAY DIFFRACTION96.02
5.6-7.050.24381910.20925538X-RAY DIFFRACTION96.16
7.05-48.590.24192060.20185539X-RAY DIFFRACTION96.08

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